Dear R-Sig-Phylo,
I’m interested in representations of ancestral recombination graphs (ARGs).
From my reading of the extended Newick format (G. Cardona et al., 2008), and
the ape/evonet documentation, it appears as if the R-base representations of
phylogenetic networks don't have a standard
Hi Russell ,
It can happen that PGLS models have difficulties to fit to the data when there
is a free parameter in the correlation structure. This is the case of
corMartins and corPagel. A way around is to set 'fixed = TRUE' when creating
these correlation structures which has the effect of
Dear Sim�n,
Typically people do this by �painting� regimes on the tree using the discrete
trait and then trying different OU models for the different regimes. For
example, does being in the island regime lead to a higher rate of evolution
(bigger sigma in the BMS model) than being in the
